Search results for: multi-time delay gene network.

Authors: Z. Saidi, A.O. Boudraa, J.C. Cexus, S. Bourennane

Abstract:

In this paper, a new time-delay estimation technique based on the cross IB-energy operator [5] is introduced. This quadratic energy detector measures how much a signal is present in another one. The location of the peak of the energy operator, corresponding to the maximum of interaction between the two signals, is the estimate of the delay. The method is a fully data-driven approach. The discrete version of the continuous-time form of the cross IBenergy operator, for its implementation, is presented. The effectiveness of the proposed method is demonstrated on real underwater acoustic signals arriving from targets and the results compared to the cross-correlation method.

Keywords: Teager-Kaiser energy operator, Cross-energyoperator, Time-Delay, Underwater acoustic signals.

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Authors: Hong Yi Huang, Wei Ti Kuo, Yi You Huang

Abstract:

Non-viral gene carriers composed of biodegradable polymers or lipids have been considered as a safer alternative for gene carriers over viral vectors. We have developed multi-functional nano-micelles for both drug and gene delivery application. Polyethyleneimine (PEI) was modified by grafting stearic acid (SA) and formulated to polymeric micelles (PEI-SA) with positive surface charge for gene and drug delivery. Our results showed that PEI-SA micelles provided high siRNA binding efficiency. In addition, siRNA delivered by PEI-SA carriers also demonstrated significantly high cellular uptake even in the presence of serum proteins. The post-transcriptional gene silencing efficiency was greatly improved by the polyplex formulated by 10k PEI-SA/siRNA. The amphiphilic structure of PEI-SA micelles provided advantages for multifunctional tasks; where the hydrophilic shell modified with cationic charges can electrostatically interact with DNA or siRNA, and the hydrophobic core can serve as payloads for hydrophobic drugs, making it a promising multifunctional vehicle for both genetic and chemotherapy application.

Keywords: polyethyleneimine, gene delivery, micelles, siRNA

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Authors: P.S. Prakash, S. Selvan

Abstract:

IP networks are evolving from data communication infrastructure into many real-time applications such as video conferencing, IP telephony and require stringent Quality of Service (QoS) requirements. A rudimentary issue in QoS routing is to find a path between a source-destination pair that satisfies two or more endto- end constraints and termed to be NP hard or complete. In this context, we present an algorithm Multi Constraint Path Problem Version 3 (MCPv3), where all constraints are approximated and return a feasible path in much quicker time. We present another algorithm namely Delay Coerced Multi Constrained Routing (DCMCR) where coerce one constraint and approximate the remaining constraints. Our algorithm returns a feasible path, if exists, in polynomial time between a source-destination pair whose first weight satisfied by the first constraint and every other weight is bounded by remaining constraints by a predefined approximation factor (a). We present our experimental results with different topologies and network conditions.

Keywords: Routing, Quality-of-Service (QoS), additive constraints, shortest path, delay coercion.

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Authors: Sergei Aleinik, Mikhail Stolbov

Abstract:

In this work, a method of time delay estimation for  dual-channel acoustic signals (speech, music, etc.) recorded under  reverberant conditions is investigated. Standard methods based on  cross-correlation of the signals show poor results in cases involving  strong reverberation, large distances between microphones and  asynchronous recordings. Under similar conditions, a method based  on cross-correlation of temporal envelopes of the signals delivers a  delay estimation of acceptable quality. This method and its properties  are described and investigated in detail, including its limits of  applicability. The method’s optimal parameter estimation and a  comparison with other known methods of time delay estimation are  also provided.

 

Keywords: Cross-correlation, delay estimation, signal envelope, signal processing.

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Authors: Syed Sohaib Bin Hasib, Hiyam Al-Kilidar

Abstract:

Meeting project deadlines is a major challenge for most construction projects. In this study, perceptions of contractors, clients, and consultants are compared relative to a list of factors derived from the review of the extant literature on project delay. 59 causes (categorized into 8 groups) of project delays were identified from the literature. A survey was devised to get insights and ranking of these factors from clients, consultants & contractors in the Australian construction industry. Findings showed that project delays in the Australian construction industry are mainly the result of skill shortages, interference in execution, and poor coordination and communication between the project stakeholders.

Keywords: Construction, delay factors, time delay, Australian construction industry.

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Authors: Apidet Booranawong, Wiklom Teerapabkajorndet

Abstract:

An enhanced ad-hoc on-demand distance vector routing (E-AODV) protocol for control system applications in wireless sensor and actuator networks (WSANs) is proposed. Our routing algorithm is designed by considering both wireless network communication and the control system aspects. Control system error and network delay are the main selection criteria in our routing protocol. The control and communication performance is evaluated on multi-hop IEEE 802.15.4 networks for building-temperature control systems. The Gilbert-Elliott error model is employed to simulate packet loss in wireless networks. The simulation results demonstrate that the E-AODV routing approach can significantly improve the communication performance better than an original AODV routing under various packet loss rates. However, the control performance result by our approach is not much improved compared with the AODV routing solution.

Keywords: WSANs, building temperature control, AODV routing protocol, control system error, settling time, delay, delivery ratio.

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Authors: Wei Wang, Dongming Peng, Honggang Wang, Hamid Sharif

Abstract:

Multirate multimedia delivery applications in multihop Wireless Mesh Network (WMN) are data redundant and delay-sensitive, which brings a lot of challenges for designing efficient transmission systems. In this paper, we propose a new cross layer resource allocation scheme to minimize the receiver side distortion within the delay bound requirements, by exploring application layer Position and Value (P-V) diversity as well as the multihop Effective Capacity (EC). We specifically consider image transmission optimization here. First of all, the maximum supportable source traffic rate is identified by exploring the multihop Effective Capacity (EC) model. Furthermore, the optimal source coding rate is selected according to the P-V diversity of multirate media streaming, which significantly increases the decoded media quality. Simulation results show the proposed approach improved media quality significantly compared with traditional approaches under the same QoS requirements.

Keywords: Multirate Multimedia Streaming, Effective CapacityMultihop Wireless Mesh Network

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Authors: Shohei Maruyama, Yasuo Matsuyama, Sachiyo Aburatani

Abstract:

Development of a method to estimate gene functions is an important task in bioinformatics. One of the approaches for the annotation is the identification of the metabolic pathway that genes are involved in. Since gene expression data reflect various intracellular phenomena, those data are considered to be related with genes’ functions. However, it has been difficult to estimate the gene function with high accuracy. It is considered that the low accuracy of the estimation is caused by the difficulty of accurately measuring a gene expression. Even though they are measured under the same condition, the gene expressions will vary usually. In this study, we proposed a feature extraction method focusing on the variability of gene expressions to estimate the genes' metabolic pathway accurately. First, we estimated the distribution of each gene expression from replicate data. Next, we calculated the similarity between all gene pairs by KL divergence, which is a method for calculating the similarity between distributions. Finally, we utilized the similarity vectors as feature vectors and trained the multiclass SVM for identifying the genes' metabolic pathway. To evaluate our developed method, we applied the method to budding yeast and trained the multiclass SVM for identifying the seven metabolic pathways. As a result, the accuracy that calculated by our developed method was higher than the one that calculated from the raw gene expression data. Thus, our developed method combined with KL divergence is useful for identifying the genes' metabolic pathway.

Keywords: Metabolic pathways, gene expression data, microarray, Kullback–Leibler divergence, KL divergence, support vector machines, SVM, machine learning.

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Authors: Changjin Xu

Abstract:

In this paper, a delayed prototype model is studied. Regarding the delay as a bifurcation parameter, we prove that a sequence of Hopf bifurcations will occur at the positive equilibrium when the delay increases. Using the normal form method and center manifold theory, some explicit formulae are worked out for determining the stability and the direction of the bifurcated periodic solutions. Finally, Computer simulations are carried out to explain some mathematical conclusions.

Keywords: Prototype model, Stability, Hopf bifurcation, Delay, Periodic solution.

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Authors: Haniza N., Md Khambari, M. N, Shahrin S., Adib M.Monzer Habbal, Suhaidi Hassan

Abstract:

Wireless ad hoc nodes are freely and dynamically self-organize in communicating with others. Each node can act as host or router. However it actually depends on the capability of nodes in terms of its current power level, signal strength, number of hops, routing protocol, interference and others. In this research, a study was conducted to observe the effect of hops count over different network topologies that contribute to TCP Congestion Control performance degradation. To achieve this objective, a simulation using NS-2 with different topologies have been evaluated. The comparative analysis has been discussed based on standard observation metrics: throughput, delay and packet loss ratio. As a result, there is a relationship between types of topology and hops counts towards the performance of ad hoc network. In future, the extension study will be carried out to investigate the effect of different error rate and background traffic over same topologies.

Keywords: NS-2, network topology, network performance, multi-hops

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Authors: Aziz Sezgin, Yuksel Hacioglu, Nurkan Yagiz

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Sliding mode controller for a vehicle active suspension system is designed in this study. The widely used quarter car model is preferred and it is aimed to improve the ride comfort of the passengers. The effect of the actuator time delay, which may arise due to the information processing, sensors or actuator dynamics, is also taken into account during the design of the controller. A sliding mode controller was designed that has taken into account the actuator time delay by using Smith predictor. The successful performance of the designed controller is confirmed via numerical results.

Keywords: Sliding mode control, active suspension system, actuator time delay.

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Authors: Dong Wan-li, Gu Nai-jie, Tu Kun, Bi Kun, Liu Gang

Abstract:

As originally designed for wired networks, TCP (transmission control protocol) congestion control mechanism is triggered into action when packet loss is detected. This implicit assumption for packet loss mostly due to network congestion does not work well in Mobile Ad Hoc Network, where there is a comparatively high likelihood of packet loss due to channel errors and node mobility etc. Such non-congestion packet loss, when dealt with by congestion control mechanism, causes poor TCP performance in MANET. In this study, we continue to investigate the impact of the interaction between transport protocols and on-demand routing protocols on the performance and stability of 802.11 multihop networks. We evaluate the important wireless networking events caused routing change, and propose a cross layer method to delay the unnecessary routing changes, only need to add a sensitivity parameter α , which represents the on-demand routing-s reaction to link failure of MAC layer. Our proposal is applicable to the plain 802.11 networking environment, the simulation results that this method can remarkably improve the stability and performance of TCP without any modification on TCP and MAC protocol.

Keywords: Mobile ad hoc networks (MANET), on-demandrouting, performance, transmission control protocol (TCP).

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Authors: J. Levendovszky, I. Koncz, P. Boros

Abstract:

The paper is concerned with developing stochastic delay mechanisms for efficient multicast protocols and for smooth mobile handover processes which are capable of preserving a given Quality of Service (QoS). In both applications the participating entities (receiver nodes or subscribers) sample a stochastic timer and generate load after a random delay. In this way, the load on the networking resources is evenly distributed which helps to maintain QoS communication. The optimal timer distributions have been sought in different p.d.f. families (e.g. exponential, power law and radial basis function) and the optimal parameter have been found in a recursive manner. Detailed simulations have demonstrated the improvement in performance both in the case of multicast and mobile handover applications.

Keywords: Multicast communication, stochactic delay mechanisms.

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Authors: Liping Jing, Michael K. Ng, Tieyong Zeng

Abstract:

Microarray data profiles gene expression on a whole genome scale, therefore, it provides a good way to study associations between gene expression and occurrence or progression of cancer. More and more researchers realized that microarray data is helpful to predict cancer sample. However, the high dimension of gene expressions is much larger than the sample size, which makes this task very difficult. Therefore, how to identify the significant genes causing cancer becomes emergency and also a hot and hard research topic. Many feature selection algorithms have been proposed in the past focusing on improving cancer predictive accuracy at the expense of ignoring the correlations between the features. In this work, a novel framework (named by SGS) is presented for stable gene selection and efficient cancer prediction . The proposed framework first performs clustering algorithm to find the gene groups where genes in each group have higher correlation coefficient, and then selects the significant genes in each group with Bayesian Lasso and important gene groups with group Lasso, and finally builds prediction model based on the shrinkage gene space with efficient classification algorithm (such as, SVM, 1NN, Regression and etc.). Experiment results on real world data show that the proposed framework often outperforms the existing feature selection and prediction methods, say SAM, IG and Lasso-type prediction model.

Keywords: Gene Selection, Cancer Prediction, Lasso, Clustering, Classification.

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Authors: A. M. Tahsini

Abstract:

Computational study of two dimensional supersonic reacting hydrogen-air flows is performed to investigate the nitrogen effects on ignition delay time for premixed and diffusion flames. Chemical reaction is treated using detail kinetics and the advection upstream splitting method is used to calculate the numerical inviscid fluxes. The results show that just in stoichiometric condition for both premixed and diffusion flames, there is monotone dependency of the ignition delay time to the nitrogen addition. In other situations, the optimal condition from ignition viewpoint should be found using numerical investigations.

Keywords: Diffusion flame, Ignition delay time, Mixing layer, Numerical simulation, Premixed flame, Supersonic flow.

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Authors: Ping He, Heng-You Lan, Gong-Quan Tan

Abstract:

The multidelays linear control systems described by difference differential equations are often studied in modern control theory. In this paper, the delay-independent stabilization algebraic criteria and the theorem of delay-independent stabilization for linear systems with multiple time-delays are established by using the Lyapunov functional and the Riccati algebra matrix equation in the matrix theory. An illustrative example and the simulation result, show that the approach to linear systems with multiple time-delays is effective.

Keywords: Linear system, Delay-independent stabilization, Lyapunovfunctional, Riccati algebra matrix equation.

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Authors: M. Sallam, A. Ramadan, M. Fanni, M. Abdellatif

Abstract:

Time delay in bilateral teleoperation system was introduced as a sufficient reason to make the system unstable or certainly degrade the system performance. In this paper, simulations and experimental results of implementing p-like control scheme, under different ranges of variable time delay, will be presented to verify a certain criteria, which guarantee the system stability and position tracking. The system consists of two Phantom premium 1.5A devices. One of them acts as a master and the other acts as a slave. The study includes deriving the Phantom kinematic and dynamic model, establishing the link between the two Phantoms over Simulink in Matlab, and verifying the stability criteria with simulations and real experiments.

Keywords: bilateral teleoperation, Phantom premium 1.5, varying time delay

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Authors: Kostas Siozios, Dimitrios Soudris, Antonios Thanailakis

Abstract:

Modern applications realized onto FPGAs exhibit high connectivity demands. Throughout this paper we study the routing constraints of Virtex devices and we propose a systematic methodology for designing a novel general-purpose interconnection network targeting to reconfigurable architectures. This network consists of multiple segment wires and SB patterns, appropriately selected and assigned across the device. The goal of our proposed methodology is to maximize the hardware utilization of fabricated routing resources. The derived interconnection scheme is integrated on a Virtex style FPGA. This device is characterized both for its high-performance, as well as for its low-energy requirements. Due to this, the design criterion that guides our architecture selections was the minimal Energy×Delay Product (EDP). The methodology is fully-supported by three new software tools, which belong to MEANDER Design Framework. Using a typical set of MCNC benchmarks, extensive comparison study in terms of several critical parameters proves the effectiveness of the derived interconnection network. More specifically, we achieve average Energy×Delay Product reduction by 63%, performance increase by 26%, reduction in leakage power by 21%, reduction in total energy consumption by 11%, at the expense of increase of channel width by 20%.

Keywords: Design Methodology, FPGA, Interconnection, Low-Energy, High-Performance, CAD tool.

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Authors: Cemil Tunc

Abstract:

In this paper, we study the instability of the zero solution to a nonlinear differential equation with variable delay. By using the Lyapunov functional approach, some sufficient conditions for instability of the zero solution are obtained.

Keywords: Instability, Lyapunov-Krasovskii functional, delay differential equation, fifth order.

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Authors: Mehran Garmehi, Yasser Mansouri

Abstract:

There are two paradigms proposed to provide QoS for Internet applications: Integrated service (IntServ) and Differentiated service (DiffServ).Intserv is not appropriate for large network like Internet. Because is very complex. Therefore, to reduce the complexity of QoS management, DiffServ was introduced to provide QoS within a domain using aggregation of flow and per- class service. In theses networks QoS between classes is constant and it allows low priority traffic to be effected from high priority traffic, which is not suitable. In this paper, we proposed a fuzzy controller, which reduced the effect of low priority class on higher priority ones. Our simulations shows that, our approach reduces the latency dependency of low priority class on higher priority ones, in an effective manner.

Keywords: QoS, Differentiated Service (DiffServ), FuzzyController, Delay.

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Authors: Rio G. L. D'Souza, K. Chandra Sekaran, A. Kandasamy

Abstract:

The goal of Gene Expression Analysis is to understand the processes that underlie the regulatory networks and pathways controlling inter-cellular and intra-cellular activities. In recent times microarray datasets are extensively used for this purpose. The scope of such analysis has broadened in recent times towards reconstruction of gene networks and other holistic approaches of Systems Biology. Evolutionary methods are proving to be successful in such problems and a number of such methods have been proposed. However all these methods are based on processing of genotypic information. Towards this end, there is a need to develop evolutionary methods that address phenotypic interactions together with genotypic interactions. We present a novel evolutionary approach, called Phenomic algorithm, wherein the focus is on phenotypic interaction. We use the expression profiles of genes to model the interactions between them at the phenotypic level. We apply this algorithm to the yeast sporulation dataset and show that the algorithm can identify gene networks with relative ease.

Keywords: Evolutionary computing, gene expression analysis, gene networks, microarray data analysis, phenomic algorithms.

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Authors: I. Boroňová, J. Bernasovská, J. Kľoc, Z. Tomková, E. Petrejčíková, S. Mačeková, J. Poráčová, M. M. Blaščáková

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Osteoporosis is a common multifactorial disease with a strong genetic component characterized by reduced bone mass and increased risk of fractures. Genetic factors play an important role in the pathogenesis of osteoporosis. The aim of our study was to identify the genotype and allele distribution of T245G polymorphism in OPG gene in Slovak postmenopausal women. A total of 200 unrelated Slovak postmenopausal women with diagnosed osteoporosis and 200 normal controls were genotyped for T245G (rs3134069) polymorphism of OPG gene. Genotyping was performed using the Custom Taqman®SNP Genotyping assays. Genotypes and alleles frequencies showed no significant differences (p=0.5551; p=0.6022). The results of the present study confirm the importance of T245G polymorphism in OPG gene in the pathogenesis of osteoporosis.

Keywords: OPG gene, osteoporosis, Real-time PCR, T245G polymorphism.

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Authors: Yassine Meraihi, Dalila Acheli, Rabah Meraihi

Abstract:

Vehicular Ad hoc Network (VANET) is a special case of Mobile Ad hoc Network (MANET) used to establish communications and exchange information among nearby vehicles and between vehicles and nearby fixed infrastructure. VANET is seen as a promising technology used to provide safety, efficiency, assistance and comfort to the road users. Routing is an important issue in Vehicular Ad Hoc Network to find and maintain communication between vehicles due to the highly dynamic topology, frequently disconnected network and mobility constraints.

This paper evaluates the performance of two most popular proactive routing protocols OLSR and DSDV in real city traffic scenario on the basis of three metrics namely Packet delivery ratio, throughput and average end to end delay by varying vehicles density and transmission range.

Keywords: DSDV, OLSR, Quality of service, Routing protocols, VANET.

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Authors: R. Balamurugan, A. M. Natarajan, K. Premalatha

Abstract:

Microarray gene expression data play a vital in biological processes, gene regulation and disease mechanism. Biclustering in gene expression data is a subset of the genes indicating consistent patterns under the subset of the conditions. Finding a biclustering is an optimization problem. In recent years, swarm intelligence techniques are popular due to the fact that many real-world problems are increasingly large, complex and dynamic. By reasons of the size and complexity of the problems, it is necessary to find an optimization technique whose efficiency is measured by finding the near optimal solution within a reasonable amount of time. In this paper, the algorithmic concepts of the Particle Swarm Optimization (PSO), Shuffled Frog Leaping (SFL) and Cuckoo Search (CS) algorithms have been analyzed for the four benchmark gene expression dataset. The experiment results show that CS outperforms PSO and SFL for 3 datasets and SFL give better performance in one dataset. Also this work determines the biological relevance of the biclusters with Gene Ontology in terms of function, process and component.

Keywords: Particle swarm optimization, Shuffled frog leaping, Cuckoo search, biclustering, gene expression data.

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Authors: Chenxi Yang, Zhouhong Li

Abstract:

This paper is concerned with an epidemic model with delay. By using the comparison theorem of the differential equation and constructing a suitable Lyapunov functional, Some sufficient conditions which guarantee the permeance and existence of a unique globally attractive positive almost periodic solution of the model are obtain. Finally, an example is employed to illustrate our result.

Keywords: Permanence, Almost periodic solution, Epidemic model, Delay, Feedback control.

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Authors: Tiancheng Lan

Abstract:

E10A is a kind of replication-defective adenovirus which carries the human endostatin gene to inhibit the growth of tumors. Kringle 5(K5) has almost the same function as angiostatin to also inhibit the growth of tumors since they are all the byproduct of the proteolytic cleavage of plasminogen. Tumor size increasing can be suppressed because both of the endostatin and K5 can restrain the angiogenesis process. Therefore, in order to improve the treatment effect on tumor, 2A peptide is used to construct a fusion gene carrying both E10A and K5. Using 2A peptide is an ideal strategy when a fusion gene is expressed because it can avoid many problems during the expression of more than one kind of protein. The overlap extension PCR is also used to connect 2A peptide with E10A and K5. The final construction of fusion gene E10A-2A-K5 can provide a possible new method of the anti-angiogenesis treatment with a better expression performance.

Keywords: E10A, Kringle 5, 2A peptide, overlap extension PCR.

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Authors: H. El-Madbouly

Abstract:

For future Broad band ISDN, Asynchronous Transfer Mode (ATM) is designed not only to support a wide range of traffic classes with diverse flow characteristics, but also to guarantee the different quality of service QOS requirements. The QOS may be measured in terms of cell loss probability and maximum cell delay. In this paper, ATM networks in which the virtual path (VP) concept is implemented are considered. By applying the Markov Deterministic process method, an efficient algorithm to compute the minimum capacity required to satisfy the QOS requirements when multiple classes of on-off are multiplexed on to a single VP. Using the result, we then proposed a simple algorithm to determine different combinations of VP to achieve the optimum of the total capacity required for satisfying the individual QOS requirements (loss- delay).

Keywords: Bandwidth allocation, Quality of services, ATMNetwork, virtual path.

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Authors: M. Miladi, T. Ezzedine, R. Bouallegue

Abstract:

In the current decade, wireless sensor networks are emerging as a peculiar multi-disciplinary research area. By this way, energy efficiency is one of the fundamental research themes in the design of Medium Access Control (MAC) protocols for wireless sensor networks. Thus, in order to optimize the energy consumption in these networks, a variety of MAC protocols are available in the literature. These schemes were commonly evaluated under simple network density and a few results are published on their robustness in realistic network-s size. We, in this paper, provide an analytical study aiming to highlight the energy waste sources in wireless sensor networks. Then, we experiment three energy efficient hybrid CSMA/CA based MAC protocols optimized for wireless sensor networks: Sensor-MAC (SMAC), Time-out MAC (TMAC) and Traffic aware Energy Efficient MAC (TEEM). We investigate these protocols with different network densities in order to discuss the end-to-end performances of these schemes (i.e. in terms of energy efficiency, delay and throughput). Through Network Simulator (NS- 2) implementations, we explore the behaviors of these protocols with respect to the network density. In fact, this study may help the multihops sensor networks designers to design or select the MAC layer which matches better their applications aims.

Keywords: Energy efficiency, medium access control, network density, wireless sensor networks.

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Authors: Caigen Zhou, Haibo Jiang

Abstract:

The problem of robust fuzzy control for a class of nonlinear fuzzy impulsive singular perturbed systems with time-varying delay is investigated by employing Lyapunov functions. The nonlinear delay system is built based on the well-known T–S fuzzy model. The so-called parallel distributed compensation idea is employed to design the state feedback controller. Sufficient conditions for global exponential stability of the closed-loop system are derived in terms of linear matrix inequalities (LMIs), which can be easily solved by LMI technique. Some simulations illustrate the effectiveness of the proposed method.

Keywords: T–S fuzzy model, singular perturbed systems, time-varying delay, robust control.

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Authors: Hong Li, Shou-Ming Zhong, Hou-Biao Li

Abstract:

In this paper, we mainly study the stability of linear and interval linear fractional systems with time delay. By applying the characteristic equations, a necessary and sufficient stability condition is obtained firstly, and then some sufficient conditions are deserved. In addition, according to the equivalent relationship of fractional order systems with order 0 < α ≤ 1 and with order 1 ≤ β < 2, one may get more relevant theorems. Finally, two examples are provided to demonstrate the effectiveness of our results.

Keywords: Fractional order systems, Time delay, Characteristic equation.

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